This study explored the association between different types of brief disagreements and subsequent levels of expressed psychological uncertainty, a fundamental cognitive aspect of complex problem solving. We examined 11 hours (11 861 utterances) of conversations in expert science teams, sampled across the first 90 days of the Mars Exploration Rover mission. Utterances were independently coded for micro‐conflicts and expressed psychological uncertainty. Using time‐lagged hierarchical linear modeling applied to blocks of 25 utterances, we found that micro‐conflicts regarding rover planning were followed by greater uncertainty. Brief disagreements about science issues were followed by an increase in expressed uncertainty early in the mission. Examining the potential reverse temporal association, uncertainty actually predicted fewer subsequent disagreements, ruling out indirect, third variable associations of conflict and uncertainty. Overall, these findings suggest that some forms of disagreement may serve to uncover important areas of uncertainty in complex teamwork, perhaps via revealing differences in mental models.Copyright © 2016 John Wiley & Sons, Ltd.